Search results for: molecular structure

Authors: Alexandre Barbosa de Almeida, Telma Woerle de Lima Soares

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Protein structure prediction is a challenging task in the bioinformatics field. The biological function of all proteins majorly relies on the shape of their three-dimensional conformational structure, but less than 1% of all known proteins in the world have their structure solved. This work proposes a deep learning model to address this problem, attempting to predict some aspects of the protein conformations. Throughout a process of multiobjective dominance, a recurrent neural network was trained to abstract the particular bias of each individual multiobjective algorithm, generating a heuristic that could be useful to predict some of the relevant aspects of the three-dimensional conformation process formation, known as protein folding.

Keywords: Ab initio heuristic modeling, multiobjective optimization, protein structure prediction, recurrent neural network

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Authors: Maedeh Rahimnejad, Bahman Vahidi, Bahman Ebrahimi Hoseinzadeh, Fatemeh Yazdian, Puria Motamed Fath, Roghieh Jamjah

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Introduction: The intensive labor and high cost of developing new vehicles for controlled drug delivery highlights the need for a change in their discovery process. Computational models can be used to accelerate experimental steps and control the high cost of experiments. Methods: In this work, to better understand the interaction of anti-cancer drug and the nanocarrier with the cell membrane, we have done molecular dynamics simulation using NAMD. We have chosen paclitaxel for the drug molecule and dipalmitoylphosphatidylcholine (DPPC) as a natural phospholipid nanocarrier. Results: Next, center of mass (COM) between molecules and the van der Waals interaction energy close to the cell membrane has been analyzed. Furthermore, the simulation results of the paclitaxel interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane have been compared. Discussion: Analysis by molecular dynamics (MD) showed that not only the energy between the nanocarrier and the cell membrane is low, but also the center of mass amount decreases in the nanocarrier and the cell membrane system during the interaction; therefore they show significantly better interaction in comparison to the individual drug with the cell membrane.

Keywords: anti-cancer drug, center of mass, interaction energy, molecular dynamics simulation, nanocarrier

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Authors: Asyraf Abdul Halim, Mohd Edil Abd Sukor, Obiyathulla Ismath Bacha

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This paper attempts to investigate the capital structure behavior of Shariah compliant firms of various levels as well those firms who are consistently Shariah non-compliant in Malaysia. The paper utilizes a unique dataset of firms of the heterogeneous level of Shariah-compliancy status over a 20 year period from the year 1997 to 2016. The paper focuses on the effects of dynamic forces behind capital structure variation such as the optimal capital structure behavior based on the trade-off, pecking order, market timing and firmly fixed effect models of capital structure. This study documents significant evidence in support of the trade-off theory with a high speed of adjustment (SOA) as well as for the time-invariant firm fixed effects across all Shariah compliance group.

Keywords: capital structure, market timing, trade-off theory, equity risk premium, Shariah-compliant firms

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Authors: V. K. Srivastava

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Graphene has recently attracted an increasing attention in nanocomposites applications because it has 200 times greater strength than steel, making it the strongest material ever tested. Graphene, as the fundamental two-dimensional (2D) carbon structure with exceptionally high crystal and electronic quality, has emerged as a rapidly rising star in the field of material science. Graphene, as defined, as a 2D crystal, is composed of monolayers of carbon atoms arranged in a honeycombed network with six-membered rings, which is the interest of both theoretical and experimental researchers worldwide. The name comes from graphite and alkene. Graphite itself consists of many graphite-sheets stacked together by weak van der Waals forces. This is attributed to the monolayer of carbon atoms densely packed into honeycomb structure. Due to superior inherent properties of graphene nanoplatelets (GnP) over other nanofillers, GnP particles were added in epoxy resin with the variation of weight percentage. It is indicated that the DMA results of storage modulus, loss modulus and tan δ, defined as the ratio of elastic modulus and imaginary (loss) modulus versus temperature were affected with addition of GnP in the epoxy resin. In epoxy resin, damping (tan δ) is usually caused by movement of the molecular chain. The tan δ of the graphene nanoplatelets/epoxy resin composite is much lower than that of epoxy resin alone. This finding suggests that addition of graphene nanoplatelets effectively impedes movement of the molecular chain. The decrease in storage modulus can be interpreted by an increasing susceptibility to agglomeration, leading to less energy dissipation in the system under viscoelastic deformation. The results indicates the tan δ increased with the increase of temperature, which confirms that tan δ is associated with magnetic field strength. Also, the results show that the nanohardness increases with increase of elastic modulus marginally. GnP filled epoxy resin gives higher value than the epoxy resin, because GnP improves the mechanical properties of epoxy resin. Debonding of GnP is clearly observed in the micrograph having agglomeration of fillers and inhomogeneous distribution. Therefore, DMA and nanohardness studies indiacte that the elastic modulus of epoxy resin is increased with the addition of GnP fillers.

Keywords: agglomeration, elastic modulus, epoxy resin, graphene nanoplatelet, loss modulus, nanohardness, storage modulus

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Authors: M. Zemouli, K. Amara, M. Elkeurti, Y. Benallou

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We present the molecular dynamic simulations results of the structural and dynamical properties of the zinc-blende GaBi over a wide range of temperature (300-1000) K. Our simulation where performed in the framework of the three-body Tersoff potential, which accurately reproduces the lattice constants and elastic constants of the GaBi. A good agreement was found between our calculated results and the available theoretical data of the lattice constant, the bulk modulus and the cohesive energy. Our study allows us to predict the thermodynamic properties such as the specific heat and the lattice thermal expansion. In addition, this method allows us to check its ability to predict the phase transition of this compound. In particular, the transition pressure to the rock-salt phase is calculated and the results are compared with other available works.

Keywords: Gallium compounds, molecular dynamics simulations, interatomic potential thermodynamic properties, structural phase transition

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Authors: Sahar Jami, Iman Valizadeh

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The purpose of the study: The aim of this study was to evaluate the influence of culture on the choice of capital structure management companies are listed in the Tehran Stock Exchange. Methods: This study was a cross-document using data after the event (Retrospective) in 1394 was performed. To select a sample of elimination sampling (screening) is used to determine the sample size was 123 companies. Results: The results showed that the variables of culture, return on equity, a significant positive impact on the capital structure (ROA, QTobins) and financial leverage and firm size variables and a significant negative impact on the capital structure (ROA, QTobins).

Keywords: culture management, capital structure, ROA, QTobins, variables of culture

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Authors: M. Dehestani, M. Ghasemi-Kooch

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In this work, adsorption of chlorophylls a and b pigments in aqueous solution on the inner and outer surfaces of single-walled carbon nanotube (SWCNT) has been studied using molecular dynamics simulation. The linear interaction energy algorithm has been used to calculate the binding free energy. The results show that the adsorption of two pigments is fine on the both positions. Although there is the close similarity between these two pigments, their interaction with the nanotube is different. This result is useful to separate these pigments from one another. According to interaction energy between the pigments and carbon nanotube, interaction between these pigments-SWCNT on the inner surface is stronger than the outer surface. The interaction of SWCNT with chlorophylls phytol tail is stronger than the interaction of SWCNT with porphyrin ring of chlorophylls.

Keywords: adsorption, chlorophyll, interaction, molecular dynamics simulation, nanotube

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Authors: M. Zemouli, K. Amara, M. Elkeurti, Y. Benallou

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We present a theoretical study of the structural, elastic and thermodynamic properties of the zinc-blende AlBi for a wide temperature range. The simulation calculation is performed in the framework of the molecular dynamics method using the three-body Tersoff potential which reproduces provide, with reasonable accuracy, the lattice constants and elastic constants. Our results for the lattice constant, the bulk modulus and cohesive energy are in good agreement with other theoretical available works. Other thermodynamic properties such as the specific heat and the lattice thermal expansion can also be predicted. In addition, this method allows us to check its ability to predict the phase transition of this compound. In particular, the transition pressure to the rock-salt phase is calculated and the results are compared with other available works.

Keywords: aluminium compounds, molecular dynamics simulations, interatomic potential, thermodynamic properties, structural phase transition

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Authors: Buntheng Chhorn, WooYoung Jung

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Large-scale swing has been used in entertainment and performance, especially in circus, for a very long time. To increase the safety of this type of structure, a thorough analysis for displacement and bearing stress was performed for an extreme condition where a full cycle swing occurs. Different masses, ranging from 40 kg to 220 kg, and velocities were applied on the swing. Then, based on the solution of differential dynamics equation, swing velocity response to harmonic force was obtained. Moreover, the resistance capacity was estimated based on ACI steel structure design guide. Subsequently, numerical analysis was performed in ABAQUS to obtain the stress on each frame of the swing. Finally, the analysis shows that the expansion of swing structure frame section was required for mass bigger than 150kg.

Keywords: swing structure, displacement, bearing stress, dynamic loads response, finite element analysis

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Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

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There are several methods for determination of the lipophilicity of biologically active compounds, however chromatography has been shown as a very suitable method for this purpose. Chromatographic (C18-RP-HPLC) analysis of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives was carried out. The obtained retention indices (logk, methanol (90%) / water (10%)) were correlated with calculated physicochemical and lipophilicity descriptors. The QSRR analysis was carried out applying principal component regression (PCR) and partial least squares regression (PLS). The PCR and PLS model were selected on the basis of the highest variance and the lowest root mean square error of cross-validation. The obtained PCR and PLS model successfully correlate the calculated molecular descriptors with logk parameter indicating the significance of the lipophilicity of compounds in chromatographic process. On the basis of the obtained results it can be concluded that the obtained logk parameters of the analyzed androstane derivatives can be considered as their chromatographic lipophilicity. These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1105.

Keywords: androstane derivatives, chromatography, molecular structure, principal component regression, partial least squares regression

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Authors: D. S. Malatesh, K. J. Ananda, C. Ansar Kamran, K. Ganesh Udupa

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Dirofilaria repens is a mosquito-borne filarioid nematode of dogs and other carnivores and accidentally affects humans. D. repens is reported in many countries, including India. Subcutaneous dirofilariosis caused by D. repens is a zoonotic disease, widely distributed throughout Europe, Asia, and Africa, with higher prevalence reported in dogs from Sri Lanka (30-60%), Iran (61%) and Italy (21-25%). Dirofilariasis in dogs was diagnosed by detection of microfilariae in blood. Identification of different Dirofilaria species was done by using molecular methods like polymerase chain reaction (PCR). Even though many researchers reported molecular evidence of D. repens across India, to our best knowledge there is no data available on molecular diagnosis of D. repens in dogs and its zoonotic implication in Karnataka state a southern state in India. The aim of the present study was to identify the Dirofilaria species occurring in dogs from Karnataka, India. Out of 310 samples screened for the presence of microfilariae using traditional diagnostic methods, 99 (31.93%) were positive for the presence of microfilariae. Based on the morphometry, the microfilariae were identified as D. repens. For confirmation of species, the samples were subjected to PCR using pan filarial primers (DIDR-F1, DIDR-R1) for amplification of internal transcribed spacer region 2 (ITS2) of the ribosomal DNA. The PCR product of 484 base pairs on agarose gel was indicative of D. repens. Hence, a single PCR reaction using pan filarial primers can be used to differentiate filarial species found in dogs. The present study confirms that dirofilarial species occurring in dogs from Karnataka is D. repens and further sequencing studies are needed for genotypic characterization of D. repens.

Keywords: Dirofilaria repens, molecular characterization, polymerase chain reaction, Karnataka, India

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Authors: Wilmer Esteban Vallejo Narváez, Serguei Fomine

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The theoretical investigation of Si-doped graphene nanoflakes (NFs) was conducted to understand their catalytic impact on CO₂ reduction using molecular hydrogen at the Density Functional Theory (DFT) level. The introduction of silicon by substituting carbon induces defects in the NF structure, resulting in a polyradical ground state. This silicon defect significantly boosts reactivity towards substrates, making Si-doped graphene NFs more catalytically active in CO₂ reduction to formic acid compared to silicene. Notably, Si-doped graphene demonstrates a preference for formic acid over carbon monoxide, mirroring the behavior of silicene. Furthermore, investigations into formic acid-to-formaldehyde and formaldehyde-to-methanol conversions reveal instances where Si-doped graphene outperforms silicene in terms of efficacy. In the final reduction step, the methanol-to-methane reaction unfolds in four stages, with the rate-determining step involving hydrogen transfer from silicon to methyl. Notably, the activation energy for this step is lower in Si-doped graphene compared to silicene. Consequently, Si-doped graphene NFs emerge as superior catalysts with lower activation energies overall. Remarkably, throughout these catalytic processes, Si-doped graphene maintains environmental stability, further highlighting its enhanced catalytic activity without compromising graphene's inherent stability.

Keywords: silicon-doped graphene, CO₂ reduction, DFT, catalysis

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Authors: M. Asghar, K. Mahmood, F. Malik, Lu Na, Y-H Xie, Yasin A. Raja, I. Ferguson

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In this paper, we have reported an enhancement in Seebeck coefficient of un-doped zinc oxide (ZnO) grown by molecular beam epitaxy (MBE) on silicon (001) substrate by annealing treatment. The grown ZnO thin films were annealed in oxygen environment at 500°C – 800°C, keeping a step of 100°C for one hour. Room temperature Seebeck measurements showed that Seebeck coefficient and power factor increased from 222 to 510 µV/K and 8.8×10^-6 to 2.6×10^-4 Wm^-1K^-2 as annealing temperature increased from 500°C to 800°C respectively. This is the highest value of Seebeck coefficient ever reported for un-doped MBE grown ZnO according to best of our knowledge. This observation was related with the improvement of crystal structure of grown films with annealing temperature. X-ray diffraction (XRD) results demonstrated that full width half maximum (FWHM) of ZnO (002) plane decreased and crystalline size increased as the annealing temperature increased. Photoluminescence study revealed that the intensity of band edge emission increased and defect emission decreased as annealing temperature increased because the density of oxygen vacancy related donor defects decreased with annealing temperature. This argument was further justified by the Hall measurements which showed a decreasing trend of carrier concentration with annealing temperature.

Keywords: ZnO, MBE, thermoelectric properties, annealing temperature, crystal structure

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Authors: Giovanni Meloni

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Recent results are presented from experiments carried out at the Advanced Light Source (ALS) at the Chemical Dynamics Beamline of Lawrence Berkeley National Laboratory using multiplexed synchrotron photoionization mass spectrometry. The reaction mixture and a buffer gas (He) are introduced through individually calibrated mass flow controllers into a quartz slow flow reactor held at constant pressure and temperature. The gaseous mixture effuses through a 650 μm pinhole into a 1.5 mm skimmer, forming a molecular beam that enters a differentially pumped ionizing chamber. The molecular beam is orthogonally intersected by a tunable synchrotron radiation produced by the ALS in the 8-11 eV energy range. Resultant ions are accelerated, collimated, and focused into an orthogonal time-of-flight mass spectrometer. Reaction species are identified by their mass-to-charge ratios and photoionization (PI) spectra. Comparison of experimental PI spectra with literature and/or simulated curves is routinely done to assure the identity of a given species. With the aid of electronic structure calculations, potential energy surface scans are performed, and Franck-Condon spectral simulations are obtained. Examples of these experiments are discussed, ranging from new intermediates characterization to reaction mechanisms elucidation and biofuels oxidation pathways identification.

Keywords: mass spectrometry, reaction intermediates, synchrotron photoionization, oxidation reactions

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Authors: M. Dehestani, F. Kamali, M. Klantari Pour, L. Zeidabadi-Nejad

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Chemical bonding between polyethylene glycol (PEG) with pharmaceutical proteins called pegylation is one of the most effective methods of improving the pharmacological properties. The covalent attachment of polyethylene glycol (PEG) to proteins will increase their pharmacologic properties. For the formation of a combination of pegylated protein should first be activated PEG and connected to the protein. Interferons(IFNs) are a family of cytokines which show antiviral effects in front of the biological and are responsible for setting safety system. In this study, the nature and properties of the interaction between active positions of IFNs and polyethylene glycol have been investigated using molecular dynamics simulation. The main aspect of this theoretical work focuses on the achievement of valuable data on the reaction pathways of PEG-IFNs and the transition state energy. Our results provide a new perspective on the interactions, chemical properties and reaction pathways between IFNs and PEG.

Keywords: interaction, interferons, molecular dynamics simulation, polyethylene glycol

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Authors: Amani Tahat, Serdal Kirmizialtin

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Trajectory fragment methods such as Markov State Models (MSM), Milestoning (MS) and Transition Path sampling are the prime choice of extending the timescale of all atom Molecular Dynamics simulations. In these approaches, a set of structures that covers the accessible phase space has to be chosen a priori using cluster analysis. Structural clustering serves to partition the conformational state into natural subgroups based on their similarity, an essential statistical methodology that is used for analyzing numerous sets of empirical data produced by Molecular Dynamics (MD) simulations. Local transition kernel among these clusters later used to connect the metastable states using a Markovian kinetic model in MSM and a non-Markovian model in MS. The choice of clustering approach in constructing such kernel is crucial since the high dimensionality of the biomolecular structures might easily confuse the identification of clusters when using the traditional hierarchical clustering methodology. Of particular interest, in the case of MS where the milestones are very close to each other, accurate determination of the milestone identity of the trajectory becomes a challenging issue. Throughout this work we present two cluster analysis methods applied to the cis–trans isomerism of dinucleotide AA. The choice of nucleic acids to commonly used proteins to study the cluster analysis is two fold: i) the energy landscape is rugged; hence transitions are more complex, enabling a more realistic model to study conformational transitions, ii) Nucleic acids conformational space is high dimensional. A diverse set of internal coordinates is necessary to describe the metastable states in nucleic acids, posing a challenge in studying the conformational transitions. Herein, we need improved clustering methods that accurately identify the AA structure in its metastable states in a robust way for a wide range of confused data conditions. The single linkage approach of the hierarchical clustering available in GROMACS MD-package is the first clustering methodology applied to our data. Self Organizing Map (SOM) neural network, that also known as a Kohonen network, is the second data clustering methodology. The performance comparison of the neural network as well as hierarchical clustering method is studied by means of computing the mean first passage times for the cis-trans conformational rates. Our hope is that this study provides insight into the complexities and need in determining the appropriate clustering algorithm for kinetic analysis. Our results can improve the effectiveness of decisions based on clustering confused empirical data in studying conformational transitions in biomolecules.

Keywords: milestoning, self organizing map, single linkage, structure clustering

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Authors: Mahdi Asghari

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The cavitation phenomenon is the formation and production of micro-bubbles and eventually the bursting of the micro-bubbles inside the liquid fluid, which results in localized high pressure and temperature, causing physical and chemical fluid changes. This pressure and temperature are predicted to be 2000 atmospheres and 5000 °C, respectively. As a result of small bubbles bursting from this process, temperature and pressure increase momentarily and locally, so that the intensity and magnitude of these temperatures and pressures provide the energy needed to break the molecular bonds of heavy compounds such as fuel oil. In this paper, we study the theory of cavitation and the methods of cavitation production by acoustic and hydrodynamic methods and the necessary mechanical equipment and reactors for industrial application of the hydrodynamic cavitation method to break down the molecular bonds of the fuel oil and convert it into useful and economical products.

Keywords: Cavitation, Hydrodynamic Cavitation, Cavitation Reactor, Fuel Oil

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Authors: Sarthak S. Salunke

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Development, as a notion, is seen in perspective of western philosophical conceptions, and the western developed nations have become a yardstick for setting up development goals for developing and underdeveloped nations around the world. This blanket term of development becomes superficial and materialistic in context of the vast geopolitical, territorial, cultural and behavioral diversities existing in countries of the Africa and the Asia, and tends to undermine the atomistic aspect of development. Indian political theories, which are often seen as religious philosophies, have inherent structure of development of human being as an individual and as a part of the society, and, in result, development of the State. These theories, primarily individualistic in nature, have a combination of altruism and rationalism which guides human beings towards constructing a collectively developed and morally sustainable society. This research focuses on the application of this Indian thought in combination of classical liberal thought to tackle the issues of development in diverse societies. The proposed restructured model of development is based on molecular individualism, instead of atomic individual approach of liberalists, which lets development modelers to target meaningful clusters for designating goals for development based on the particular needs based on geopolitical, cultural and ethical requirements, and making it meaningful in conjunction with global development to establish a harmony between western and eastern worlds.

Keywords: Indian political thought, development, liberalism, molecular individualism

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Authors: A. Rezaei, M. Huisman, W. Van Paepegem

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Atomic interactions in molecular systems are mainly studied by particle mechanics. Nevertheless, researches have also put on considerable effort to simulate them using continuum methods. In early 2000, simple equivalent finite element models have been developed to study the mechanical properties of carbon nanotubes and graphene in composite materials. Afterward, many researchers have employed similar structural simulation approaches to obtain mechanical properties of nanostructured materials, to simplify interface behavior of fiber-reinforced composites, and to simulate defects in carbon nanotubes or graphene sheets, etc. These structural approaches, however, are limited to small deformations due to complicated local rotational coordinates. This article proposes a method for the finite element simulation of molecular mechanics. For ease in addressing the approach, here it is called Structural Finite Element Molecular Modeling (SFEMM). SFEMM method improves the available structural approaches for large deformations, without using any rotational degrees of freedom. Moreover, the method simulates molecular conformation, which is a big advantage over the previous approaches. Technically, this method uses nonlinear multipoint constraints to simulate kinematics of the atomic multibody interactions. Only truss elements are employed, and the bond potentials are implemented through constitutive material models. Because the equilibrium bond- length, bond angles, and bond-torsion potential energies are intrinsic material parameters, the model is independent of initial strains or stresses. In this paper, the SFEMM method has been implemented in ABAQUS finite element software. The constraints and material behaviors are modeled through two Fortran subroutines. The method is verified for the bond-stretch, bond-angle and bond-torsion of carbon atoms. Furthermore, the capability of the method in the conformation simulation of molecular structures is demonstrated via a case study of a graphene sheet. Briefly, SFEMM builds up a framework that offers more flexible features over the conventional molecular finite element models, serving the structural relaxation modeling and large deformations without incorporating local rotational degrees of freedom. Potentially, the method is a big step towards comprehensive molecular modeling with finite element technique, and thereby concurrently coupling an atomistic domain to a solid continuum domain within a single finite element platform.

Keywords: finite element, large deformation, molecular mechanics, structural method

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Authors: Bakhtishod Matmuratov, Sakhiba Madraximova, Rakhmat Esanov, Alimjan Matchanov

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Studies have been performed to obtain complexes of glycyrrhizic acid and kinetins in a 2:1 ratio. The complex of glycyrrhizic acid and kinetins in a 2:1 ratio was considered evidence of the formation of a molecular complex by determining the molecular masses using chromato-mass spectroscopy and analyzing the IR spectra.

Keywords: monoammonium salt of glycyrrhizic acid, glycyrrhizic acid, supramolecular complex, isomolar series, IR spectroscopy

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Authors: HoYoung Son, DongHoon Shin, WooYoung Jung

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This study presented the seismic fragility framework of concrete weir structure subjected to strong seismic ground motions and in particular, concrete aging condition of the weir structure was taken into account in this study. In order to understand the influence of concrete aging on the weir structure, by using probabilistic risk assessment, the analytical seismic fragility of the weir structure was derived for pre- and post-deterioration of concrete. The performance of concrete weir structure after five years was assumed for the concrete aging or deterioration, and according to after five years’ condition, the elastic modulus was simply reduced about one–tenth compared with initial condition of weir structures. A 2D nonlinear finite element analysis was performed considering the deterioration of concrete in weir structures using ABAQUS platform, a commercial structural analysis program. Simplified concrete degradation was resulted in the increase of almost 45% of the probability of failure at Limit State 3, in comparison to initial construction stage, by analyzing the seismic fragility.

Keywords: weir, FEM, concrete, fragility, aging

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Authors: Bing Lu, Shuang Li, Hongyuan Zhou

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The steel–concrete hybrid structure has been extensively employed in high–rise buildings and super high–rise buildings. The light gauge steel–concrete hybrid structure, including light gauge steel structure and concrete hybrid structure, is a new–type steel–concrete hybrid structure, which possesses some advantages of light gauge steel structure and concrete hybrid structure. The seismic behavior and loss assessment of three high–rise buildings with three different concrete hybrid structures were investigated through finite element software, respectively. The three concrete hybrid structures are reinforced concrete column–steel beam (RC‒S) hybrid structure, concrete–filled steel tube column–steel beam (CFST‒S) hybrid structure, and tubed concrete column–steel beam (TC‒S) hybrid structure. The nonlinear time-history analysis of three high–rise buildings under 80 earthquakes was carried out. After simulation, it indicated that the seismic performances of three high–rise buildings were superior. Under extremely rare earthquakes, the maximum inter–storey drifts of three high–rise buildings are significantly lower than 1/50. The inter–storey drift and floor acceleration of high–rise building with CFST‒S hybrid structure were bigger than those of high–rise buildings with RC‒S hybrid structure, and smaller than those of high–rise building with TC‒S hybrid structure. Then, based on the time–history analysis results, the post-earthquake repair cost ratio and repair time of three high–rise buildings were predicted through an economic performance analysis method proposed in FEMA‒P58 report. Under frequent earthquakes, basic earthquakes and rare earthquakes, the repair cost ratio and repair time of three high-rise buildings were less than 5% and 15 days, respectively. Under extremely rare earthquakes, the repair cost ratio and repair time of high-rise buildings with TC‒S hybrid structure were the most among three high rise buildings. Due to the advantages of CFST-S hybrid structure, it could be extensively employed in high-rise buildings subjected to earthquake excitations.

Keywords: seismic behavior, loss assessment, light gauge steel–concrete hybrid structure, high–rise building, time–history analysis

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Authors: M. Shahina, K. Fakruddin, C. M. Subhan, S. Rangappa

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In this work, two mixtures with equal concentrations of 1) 4ꞌ-(6-(4-(pentylamino) methyl)-3-hydroxyphenoxy) hexyloxy) biphenyl-4-carbonitrile+-4-((4-(hexyloxy) benzylidene) amino) phenyl 4-butoxy benzoate and 2) 4ꞌ - (6-(4-(hexylamino) methyl)-3-hydroxyphenoxy) hexyloxy) biphenyl-4-carbonitrile+-4-((4-(octyloxy) benzylidene) amino) phenyl 4-butoxy benzoate, have been prepared. The transition temperature and optical texture are observed by using thermal microscopy. Density and birefringence studies are carried out on the above liquid crystalline mixtures. Using density and refractive indices data, the molecular polarizabilities are evaluated by using well-known Vuks and Neugebauer models. The molecular polarizability is also evaluated theoretically by Lippincott δ function model. The results reveal that the polarizability values are same in both experimental and theoretical methods.

Keywords: liquid crystals, optical textures, transition temperature, birefringence, polarizability

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Authors: Raouf Mbarki, Fadi Al Khatib, Malek Adouni

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Knee collateral ligaments play a significant role in restraining excessive frontal motion (varus/valgus rotations). In this investigation, a multiscale frame was developed based on structural hierarchies of the collateral ligaments starting from the bottom (tropocollagen molecule) to up where the fibred reinforced structure established. Experimental data of failure tensile test were considered as the principal driver of the developed model. This model was calibrated statistically using Bayesian calibration due to the high number of unknown parameters. Then the model is scaled up to fit the real structure of the collateral ligaments and simulated under realistic boundary conditions. Predications have been successful in describing the observed transient response of the collateral ligaments during tensile test under pre- and post-damage loading conditions. Collateral ligaments maximum stresses and strengths were observed near to the femoral insertions, a results that is in good agreement with experimental investigations. Also for the first time, damage initiation and propagation were documented with this model as a function of the cross-link density between tropocollagen molecules.

Keywords: multiscale model, tropocollagen, fibrils, ligaments commas

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Authors: Sumit Sharma, Rakesh Chandra, Pramod Kumar, Navin Kumar

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Molecular dynamics (MD) simulation has been used to study the effect of carbon nanofiber (CNF) volume fraction (Vf) and aspect ratio (l/d) on mechanical properties of CNF reinforced polypropylene (PP) composites. Materials Studio 5.5 has been used as a tool for finding the modulus and damping in composites. CNF composition in PP was varied by volume from 0 to 16%. Aspect ratio of CNF was varied from l/d=5 to l/d=100. To the best of the knowledge of the authors, till date there is no study, either experimental or analytical, which predict damping for CNF-PP composites at the nanoscale. Hence, this will be a valuable addition in the area of nanocomposites. Results show that with only 2% addition by volume of CNF in PP, E11 increases 748%. Increase in E22 is very less in comparison to the increase in E11. With increase in CNF aspect ratio (l/d) till l/d=60, the longitudinal loss factor (η11) decreases rapidly. Results of this study have been compared with those available in literature.

Keywords: carbon nanofiber, elasticity, mechanical properties, molecular dynamics

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Authors: Luthfi Assholam Solamat

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Nowadays many people do not know the soil failure pattern as an important part in planning the under structure caused by the loading occurs. This is because the soil is located under the foundation, so it cannot be seen directly. Based on this study, the idea occurs to do a study for testing the soil failure pattern, especially the type of sand soil under the foundation. The necessity of doing this to the design of building structures on the land which is the initial part of the foundation structure that met with waves/vibrations during an earthquake. If the underground structure is not strong it is feared the building thereon more vulnerable to the risk of building damage. This research focuses on the search of soil failure pattern, which the most applicable in the field with the loading periodic re-testing of a particular time with the help of the integrated video visual observations performed. The results could be useful for planning under the structure in an effort to try the upper structure is minimal risk of the earthquake.

Keywords: soil failure pattern, earthquake, under structure, sand soil testing method

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Authors: Suresh Narayana, Chaitanya Akkannavar

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Assessment of behavior of reinforced concrete structures subjected to fire load, and its behavior for the multi-floor fire have been presented in this paper. This research is the part of the study to evaluate the performance of ten storied RC structure when it is subjected to fire loads at multiple floors and to evaluate the post-fire effects on structure such as deflection and stresses occurring due to combined effect of static and thermal loading. Thermal loading has been assigned to different floor levels to estimate the critical floors that initiate the collapse of the structure. The structure has been modeled and analyzed in Solid Works and commercially available Finite Element Software ABAQUS. Results are analyzed, and particular design solution has been suggested.

Keywords: collapse mechanism, fire analysis, RC structure, stress vs temperature

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Authors: Fateh Adhnouss, Husam El-Asfour, Kenneth McIsaac, AbdulMutalib Wahaishi, Idris El-Feghia

Abstract:

Conceptualization is an essential component of semantic ontology-based approaches. There have been several approaches that rely on extensional structure and extensional reduction structure in order to construct conceptualization. In this paper, several limitations are highlighted relating to their applicability to the construction of conceptualizations in dynamic and open environments. These limitations arise from a number of strong assumptions that do not apply to such environments. An intensional structure is strongly argued to be a natural and adequate modeling approach. This paper presents a conceptualization structure based on property relations and propositions theory (PRP) to the model ontology that is suitable for open environments. The model extends the First-Order Logic (FOL) notation and defines the formal representation that enables interoperability between software systems and supports semantic integration for software systems in open, dynamic environments.

Keywords: conceptualization, ontology, extensional structure, intensional structure

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Authors: Maria Fontenele, Claude-Gilles Dussap, Vincent Dumouilla, Baptiste Boit

Abstract:

Roquette Frères is a producer of plant-based ingredients that employs many processes to extract relevant molecules and often transforms them through chemical and physical processes to create desired ingredients with specific functionalities. In this context, Roquette encounters numerous multi-component complex systems in their processes, including fibers, proteins, and carbohydrates, in an aqueous environment. To develop, control, and optimize both new and old processes, Roquette aims to develop new in silico tools. Currently, Roquette uses process modelling tools which include specific thermodynamic models and is willing to develop computational methodologies such as molecular dynamics simulations to gain insights into the complex interactions in such complex media, and especially hydrogen bonding interactions. The issue at hand concerns aqueous mixtures of polyols with high dry matter content. The polyols mannitol and sorbitol molecules are diastereoisomers that have nearly identical chemical structures but very different physicochemical properties: for example, the solubility of sorbitol in water is 2.5 kg/kg of water, while mannitol has a solubility of 0.25 kg/kg of water at 25°C. Therefore, predicting liquid-solid equilibrium properties in this case requires sophisticated solution models that cannot be based solely on chemical group contributions, knowing that for mannitol and sorbitol, the chemical constitutive groups are the same. Recognizing the significance of solvation phenomena in polyols, the GePEB (Chemical Engineering, Applied Thermodynamics, and Biosystems) team at Institut Pascal has developed the COSMO-UCA model, which has the structural advantage of using quantum mechanics tools to predict formation and phase equilibrium properties. In this work, we use molecular dynamics simulations to elucidate the behavior of polyols in aqueous solution. Specifically, we employ simulations to compute essential metrics such as radial distribution functions and hydrogen bond autocorrelation functions. Our findings illuminate a fundamental contrast: sorbitol and mannitol exhibit disparate hydrogen bond lifetimes within aqueous environments. This observation serves as a cornerstone in elucidating the divergent physicochemical properties inherent to each compound, shedding light on the nuanced interplay between their molecular structures and water interactions. We also present a methodology to predict the physicochemical properties of complex solutions, taking as sole input the three-dimensional structure of the molecules in the medium. Finally, by developing knowledge models, we represent some physicochemical properties of aqueous solutions of sorbitol and mannitol.

Keywords: COSMO models, hydrogen bond, molecular dynamics, thermodynamics

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Authors: Amanda C. Evans

Abstract:

Enabling technologies such as continuous processing (CP) approaches can provide the tools needed to control and manipulate reactivities and transform chemical reactions into micro-controlled in-flow processes. Traditional synthetic approaches can be radically transformed by the application of CP, facilitating the pairing of chemical methodologies with technologies from other disciplines. CP supports sustainable processes that controllably generate reaction specificity utilizing supramolecular interactions. Continuous photochemical processing is an emerging field of investigation. The use of light to drive chemical reactivity is not novel, but the controlled use of specific and tunable wavelengths of light to selectively generate molecular structure under continuous processing conditions is an innovative approach towards chemical synthesis. This investigation focuses on the use of circularly polarized (cp) light as a sustainable catalyst for the CP generation of asymmetric molecules. Chiral photolysis has already been achieved under batch, solid-phase conditions: using synchrotron-sourced cp light, asymmetric photolytic selectivities of up to 4.2% enantiomeric excess (e.e.) have been reported. In order to determine the optimal wavelengths to use for irradiation with cp light for any given molecular building block, CD and anisotropy spectra for each building block of interest have been generated in two different solvents (water, hexafluoroisopropanol) across a range of wavelengths (130-400 nm). These spectra are being used to support a series of CP experiments using cp light to generate enantioselectivity.

Keywords: anisotropy, asymmetry, flow chemistry, active pharmaceutical ingredients

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